HudsonFst.prof: HudsonFst.prof

In fst4pg: Genetic Distance Segmentation for Population Genetics

HudsonFst.prof

Description

Perform FST profiling between pairs of pops, as requested by Contrast. If no contrast is provided, all pairs are considered

Usage

HudsonFst.prof(
  HFst.m,
  Contrast = NULL,
  Kmax = 100,
  NbSegCrit = "biggest.S3IB",
  parallel = TRUE
)

Arguments

HFst.m	A list of data.frame with two columns each, Fst and Weight, as provided by the HudsonFst.m function
Contrast	a list of two vectors with the names of the populations to be contrasted
Kmax	maximum number of breakpoints to be considered
NbSegCrit	the criterion used for the choice of the number of segments
parallel	a boolean, should the profiling be parallelized (using future) or not

Value

a smoothed profile

Examples

data(Freq);data(NbGamete)
FreqNbG <- BuildFreqNbG(Freq,NbGamete)
HFst.m <- HudsonFst.m(FreqNbG)

## Two population analysis
TwoPops <- list(First="Colombian",Second="Tuscan")
HFst.prof <- HudsonFst.prof(HFst.m,Contrast=TwoPops)

## The full example execution takes a few seconds.
## Two sets of populations to contrast

Contrast <- list(America=c("Colombian","Maya"),Europe=c("Tuscan","Italian"))
Profiles <- HudsonFst.prof(HFst.m,Contrast=Contrast)

## For larger lists and/or larger marker sets, 
## use the future package for parallel computation:

future::plan("multisession",workers=4)
Profiles <- HudsonFst.prof(HFst.m,Contrast=Contrast)
future::plan("default")

fst4pg documentation built on July 4, 2022, 1:06 a.m.